2022-10-23
Henrick et al. 2021: Bifidobacteria-mediated immune system imprinting early in life
Focus in this data analysis:
Two TSV files:
Family meta data
## sample.id baby_id family_id gestational_age group sex ## 1 2600164312 360 167 280 Term 1 ## 2 2600100341 162 69 278 Term 0 ## 3 2600100455 285 140 273 Term 0
## mode_delivery Days_after_birth Month_of_life f__Methanobacteriaceae ## 1 Vaginal 0 0 0 ## 2 Planned_C-section 1 0 0 ## 3 Vaginal 1 0 0
## f__Actinomycetaceae f__Bifidobacteriaceae f__Candidatus_Nanopelagicaceae ## 1 0.03489 1.62129 0 ## 2 0.00188 0.42010 0 ## 3 0.00000 0.46499 0
Bifido meta data
## sample.id baby_id family_id gestational_age group sex ## 1 2600164312 360 167 280 Term 1 ## 2 2600100341 162 69 278 Term 0 ## 3 2600100455 285 140 273 Term 0
## mode_delivery Days_after_birth Month_of_life g__Bifidobacterium ## 1 Vaginal 0 0 1.62129 ## 2 Planned_C-section 1 0 0.42010 ## 3 Vaginal 1 0 0.46499
## g__Bifidobacterium.s__Bifidobacterium_adolescentis ## 1 0.02872 ## 2 0.02965 ## 3 0.00147
Family data:
## weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae ## 1 1 0 0.03489 1.62129 ## 2 1 0 0.00188 0.42010 ## 3 1 0 0.00000 0.46499 ## 4 1 0 0.00000 0.25688 ## 5 1 0 0.01905 1.01351
Bifido data:
## weeks B_adolescentis B_angulatum B_animalis ## 1 1 0.02872 0 0.00000 ## 2 1 0.02965 0 0.01920 ## 3 1 0.00147 0 0.00000 ## 4 1 0.04929 0 0.00000 ## 5 1 0.02277 0 0.04185
Family vaginal data:
Filter for vaginal
## sample.id baby_id family_id gestational_age group sex mode_delivery ## 1 2600164312 360 167 280 Term 1 Vaginal ## 2 2600100455 285 140 273 Term 0 Vaginal ## 3 2600100500 23 21 278 Term 0 Vaginal
Bin by weeks and clean-up
## weeks Methanobacteriaceae Actinomycetaceae Bifidobacteriaceae ## 1 1 0 0.03489 1.62129 ## 2 1 0 0.00000 0.46499 ## 3 1 0 0.00000 1.05293
Same steps were performed with filtering for C-section
Bifido C-section data:
Filter for C-section
## sample.id baby_id family_id group sex mode_delivery ## 1 2600100341 162 69 Term 0 Planned_C-section ## 2 2600100458 276 137 Term 1 Planned_C-section ## 3 2600100460 270 135 Term 0 Planned_C-section
Bin by weeks and clean-up
## weeks B_adolescentis B_angulatum B_animalis ## 1 1 0.02965 0 0.01920 ## 2 1 0.04929 0 0.00000 ## 3 1 0.02277 0 0.04185
Same steps were performed with filtering for Vaginal
Bifido heatmap data: Keeping baby ID when binning
## weeks baby_id g__Bifidobacterium B_adolescentis ## 1 1 360 1.62129 0.02872 ## 2 1 162 0.42010 0.02965 ## 3 1 285 0.46499 0.00147 ## 4 1 276 0.25688 0.04929 ## 5 1 270 1.01351 0.02277 ## 6 1 174 95.79804 0.00000 ## 7 1 147 23.07769 0.00000 ## 8 1 138 0.30136 0.13661 ## 9 1 23 1.05293 0.00159 ## 10 1 382 0.00000 0.00000
Exploring the data:
Calculating the relative abundance at family level. Families with mean ≤ 2% were merged into ‘Other’
Splitting the previous plot into Vaginal and C-section births
Calculating the relative abundance at Bifidobacterium species level. Species with mean ≤ 2% were merged into ‘Other’
Splitting the previous plot into Vaginal and C-section births
Impact?